diff --git a/documentation/competitions/AortaSeg24.md b/documentation/competitions/AortaSeg24.md new file mode 100644 index 000000000..9e0c3526e --- /dev/null +++ b/documentation/competitions/AortaSeg24.md @@ -0,0 +1,46 @@ +Authors: \ +Maximilian Rokuss, Michael Baumgartner, Yannick Kirchhoff, Klaus H. Maier-Hein*, Fabian Isensee* + +*: equal contribution + +Author Affiliations:\ +Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg \ +Helmholtz Imaging + +# Introduction + +This document describes our submission to the [AortaSeg24 Challenge](hhttps://aortaseg24.grand-challenge.org/). +Our model is essentially a nnU-Net ResEnc L with modified data augmentation. We disable left/right mirroring and use the heavy data augmentation [DA5 Trainer](../../nnunetv2/training/nnUNetTrainer/variants/data_augmentation/nnUNetTrainerDA5.py). Training was performed on an A100 40GB GPU. + +# Experiment Planning and Preprocessing +After converting the data into the [nnUNet format](../../../nnUNet/documentation/dataset_format.md) (either keep and just rename the .mha files or convert them to .nii.gz), you can run the preprocessing: + +```bash +nnUNetv2_plan_and_preprocess -d 610 -c 3d_fullres -pl nnUNetPlannerResEncL -np 16 +``` + +# Training +We train our model using: + +```bash +nnUNetv2_train 610 3d_fullres all -p nnUNetResEncUNetLPlans -tr nnUNetTrainer_onlyMirror01_DA5 +``` +Models are trained from scratch. We train one model using all the images and a five fold cross validation ensemble for the submission. + +We recommend to increase the number of processes used for data augmentation. Otherwise you can run into CPU bottlenecks. +Use `export nnUNet_n_proc_DA=32` or higher (if your system permits!). + +# Inference +For inference you can use the default [nnUNet inference functionalities](../../../nnUNet/documentation/how_to_use_nnunet.md). Specifically, once the training is finished, run: + +```bash +nnUNetv2_predict_from_modelfolder -i INPUT_FOLDER -o OUTPUT_FOLDER -m MODEL_FOLDER -f all +``` + +for the single model trained on all the data and + +```bash +nnUNetv2_predict_from_modelfolder -i INPUT_FOLDER -o OUTPUT_FOLDER -m MODEL_FOLDER +``` + +for the five fold ensemble. \ No newline at end of file diff --git a/nnunetv2/training/nnUNetTrainer/variants/competitions/__init__.py b/nnunetv2/training/nnUNetTrainer/variants/competitions/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/nnunetv2/training/nnUNetTrainer/variants/competitions/aortaseg24.py b/nnunetv2/training/nnUNetTrainer/variants/competitions/aortaseg24.py new file mode 100644 index 000000000..2812c4a05 --- /dev/null +++ b/nnunetv2/training/nnUNetTrainer/variants/competitions/aortaseg24.py @@ -0,0 +1,5 @@ +from nnunetv2.training.nnUNetTrainer.variants.data_augmentation.nnUNetTrainerNoMirroring import nnUNetTrainer_onlyMirror01 +from nnunetv2.training.nnUNetTrainer.variants.data_augmentation.nnUNetTrainerDA5 import nnUNetTrainerDA5 + +class nnUNetTrainer_onlyMirror01_DA5(nnUNetTrainer_onlyMirror01, nnUNetTrainerDA5): + pass